1. I would recommend to use Molprobity on the website: http://molprobity.biochem.duke.edu/ 2. Remember that if your spacegroup is P1, the origin (i.e. translations along a, b and c) is not determined and the first molecule may be placed anywhere. Similarly, in monoclinic spacegroups, the translation along b. is not determined.
Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij On 9 Jun 2011, at 09:46, Ting-Wei Jiang wrote: > Dear experts, > I got two questions regarding refinement and structure determination by MR. > > 1.I got a dataset of resolution at 2A refined to Rvalue~20% and Rfree~24% > I want to know if there is any program in CCP4 could help me to check the > refined structure in detail. > For example,the model statistics in CNS could list some information that > infer band,angle violation...etc > Or I should ask what do I need to check before submitting to PDB. > > 2.A dataset of resolution collected to 2.2A is from native protein crystal(A) > and its complex form(A'+B) > whose PDB code is 2QN5 was already determined by MR(use another protein as > search model).I planned > to use A' as search model but the A' looks broken. > This number of molecules in AU was predicted to 4~6 using Mathews > coefficient. > N/a M.C. solvent% > 4 2.99 58.92 > 5 2.39 48.65 > 6 1.99 38.38 > The coordinate or orientation of output pdb(as attached figure) from MR are > always different since I changed > parameter,such as different resolution,Multi copy,search mode...etc. even > the contrast value of every run > is pretty high(>>3) > I really don't what happened with this dataset and any suggestion would be > greatly appreciated. > > > <output-pdb.png>
